[2024-01-24 10:57:13,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d7a393a-be7c-457e-b584-c226b2fe1449/dqc_reference
[2024-01-24 10:57:14,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,619] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg36c39c44-9a06-4316-bc06-92df39449002/GCF_015471425.1_ASM1547142v1_genomic.fna.gz | prodigal -d GCF_015471425.1_ASM1547142v1_genomic.fna/cds.fna -a GCF_015471425.1_ASM1547142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:36,360] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:36,360] [INFO] Task started: HMMsearch
[2024-01-24 10:57:36,360] [INFO] Running command: hmmsearch --tblout GCF_015471425.1_ASM1547142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d7a393a-be7c-457e-b584-c226b2fe1449/dqc_reference/reference_markers.hmm GCF_015471425.1_ASM1547142v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:36,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:36,758] [INFO] Found 6/6 markers.
[2024-01-24 10:57:36,818] [INFO] Query marker FASTA was written to GCF_015471425.1_ASM1547142v1_genomic.fna/markers.fasta
[2024-01-24 10:57:36,818] [INFO] Task started: Blastn
[2024-01-24 10:57:36,819] [INFO] Running command: blastn -query GCF_015471425.1_ASM1547142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7a393a-be7c-457e-b584-c226b2fe1449/dqc_reference/reference_markers.fasta -out GCF_015471425.1_ASM1547142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:37,850] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:37,853] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:37,854] [INFO] Target genome list was writen to GCF_015471425.1_ASM1547142v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:37,878] [INFO] Task started: fastANI
[2024-01-24 10:57:37,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg36c39c44-9a06-4316-bc06-92df39449002/GCF_015471425.1_ASM1547142v1_genomic.fna.gz --refList GCF_015471425.1_ASM1547142v1_genomic.fna/target_genomes.txt --output GCF_015471425.1_ASM1547142v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,365] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d7a393a-be7c-457e-b584-c226b2fe1449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d7a393a-be7c-457e-b584-c226b2fe1449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,381] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:58:01,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:01,382] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	100.0	1938	1939	95	conclusive
Pseudomonas cichorii	strain=DSM 50259	GCA_018343775.1	36746	36746	suspected-type	True	99.9993	1937	1939	95	conclusive
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	99.9888	1928	1939	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	83.2986	1157	1939	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	83.1531	1194	1939	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	83.1441	1194	1939	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	82.9296	1157	1939	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	82.8716	1193	1939	95	below_threshold
Pseudomonas avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	82.862	1137	1939	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=CFBP 1702	GCA_000935765.1	251701	251701	pathovar	True	82.7842	1224	1939	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	82.7746	1205	1939	95	below_threshold
Pseudomonas cannabina	strain=ICMP 15200	GCA_001401375.1	86840	86840	pathovar	True	82.6186	1087	1939	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	80.6504	921	1939	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	80.3725	753	1939	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	80.2955	798	1939	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	80.2057	734	1939	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	80.1899	746	1939	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	79.9189	703	1939	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	79.3425	567	1939	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,383] [INFO] DFAST Taxonomy check result was written to GCF_015471425.1_ASM1547142v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,383] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d7a393a-be7c-457e-b584-c226b2fe1449/dqc_reference/checkm_data
[2024-01-24 10:58:01,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:01,442] [INFO] Task started: CheckM
[2024-01-24 10:58:01,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015471425.1_ASM1547142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015471425.1_ASM1547142v1_genomic.fna/checkm_input GCF_015471425.1_ASM1547142v1_genomic.fna/checkm_result
[2024-01-24 10:59:03,872] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:03,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:03,896] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:03,897] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:03,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015471425.1_ASM1547142v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:03,898] [INFO] Task started: Blastn
[2024-01-24 10:59:03,898] [INFO] Running command: blastn -query GCF_015471425.1_ASM1547142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7a393a-be7c-457e-b584-c226b2fe1449/dqc_reference/reference_markers_gtdb.fasta -out GCF_015471425.1_ASM1547142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:05,671] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:05,675] [INFO] Selected 5 target genomes.
[2024-01-24 10:59:05,676] [INFO] Target genome list was writen to GCF_015471425.1_ASM1547142v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:05,681] [INFO] Task started: fastANI
[2024-01-24 10:59:05,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg36c39c44-9a06-4316-bc06-92df39449002/GCF_015471425.1_ASM1547142v1_genomic.fna.gz --refList GCF_015471425.1_ASM1547142v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015471425.1_ASM1547142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:13,954] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:13,959] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:13,959] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_018343775.1	s__Pseudomonas_E cichorii	99.9993	1937	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.65	99.06	0.98	0.95	8	conclusive
GCF_018968705.1	s__Pseudomonas_E cichorii_C	94.5597	1725	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.11	0.91	0.89	3	-
GCF_015471405.1	s__Pseudomonas_E cichorii_D	92.3417	1769	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.41	0.90	0.90	2	-
GCF_017165745.1	s__Pseudomonas_E capsici	92.0141	1707	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	97.35	0.95	0.93	13	-
GCF_003700275.1	s__Pseudomonas_E cichorii_B	87.9958	1628	1939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:13,961] [INFO] GTDB search result was written to GCF_015471425.1_ASM1547142v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:13,961] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:13,965] [INFO] DFAST_QC result json was written to GCF_015471425.1_ASM1547142v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:13,965] [INFO] DFAST_QC completed!
[2024-01-24 10:59:13,965] [INFO] Total running time: 0h2m1s